Skip to main content

Visualizations for statistical modelsof biomolecular dynamics.

Project description

b'MSMExplorer: data visualizations for biomolecular dynamics'
b'=========================================================='
b''
b'|Build Status| |Build status| |Coverage Status| |PyPI version| |License|'
b'|Documentation| |DOI|'
b''
b'.. raw:: html'
b''
b' <div class="row">'
b''
b'.. raw:: html'
b''
b' </div>'
b''
b'MSMExplorer is a Python visualization library for statistical models of'
b'biomolecular dynamics. It provides a high-level interface for drawing'
b'attractive statistical graphics with'
b'`MSMBuilder <http://msmbuilder.org>`__.'
b''
b'Documentation'
b'-------------'
b''
b'Online documentation is available'
b'`here <http://msmbuilder.org/msmexplorer/>`__. It includes IPython'
b'notebooks, detailed API documentation, and other useful info.'
b''
b'There are docs for the development version'
b'`here <http://msmbuilder.org/msmexplorer/development>`__. These should'
b'correspond with the github master branch.'
b''
b'Examples'
b'--------'
b''
b'.. code:: python'
b''
b' from msmbuilder.example_datasets import FsPeptide'
b' from msmbuilder.featurizer import RMSDFeaturizer'
b''
b' import msmexplorer as msme'
b''
b' # Load Fs Peptide Data'
b' traj = FsPeptide().get().trajectories[0]'
b''
b' # Calculate RMSD'
b' featurizer = RMSDFeaturizer(reference_traj=traj[0])'
b' rmsd = featurizer.partial_transform(traj).flatten()'
b''
b' # Plot Trace'
b" msme.plot_trace(rmsd, label='traj0', xlabel='Timestep', ylabel='RMSD (nm)')"
b''
b'.. figure:: http://msmbuilder.org/msmexplorer/development/_images/plot_trace.png'
b' :alt: '
b''
b'The documentation has an `example'
b'gallery <http://msmbuilder.org/msmexplorer/development/examples/>`__'
b'with short scripts showing how to use different parts of the package.'
b''
b'Dependencies'
b'------------'
b''
b'- Python 3.4+'
b''
b'Mandatory'
b'~~~~~~~~~'
b''
b'The latest versions of the following packages are required:'
b''
b'- `numpy <http://www.numpy.org/>`__'
b''
b'- `scipy <http://www.scipy.org/>`__'
b''
b'- `matplotlib <matplotlib.sourceforge.net>`__'
b''
b'- `networkx <https://networkx.github.io/>`__'
b''
b'- `pandas <http://pandas.pydata.org/>`__'
b''
b'- `seaborn <https://stanford.edu/~mwaskom/software/seaborn/>`__'
b''
b'- `statsmodels <http://statsmodels.sourceforge.net/devel/>`__'
b''
b'- `corner <http://corner.readthedocs.io/en/latest/>`__'
b''
b'- `mdtraj <https://mdtraj.org/>`__'
b''
b'- `msmbuilder <https://msmbuilder.org>`__'
b''
b'Installation'
b'------------'
b''
b'The preferred installation mechanism for ``msmexplorer`` is with'
b'``conda``:'
b''
b'.. code:: bash'
b''
b' $ conda install -c omnia msmexplorer'
b''
b"If you don't have conda, or are new to scientific python, we recommend"
b'that you download the `Anaconda scientific python'
b'distribution <https://store.continuum.io/cshop/anaconda/>`__.'
b''
b'To install from PyPI, just do:'
b''
b'::'
b''
b' pip install msmexplorer'
b''
b'You may instead want to use the development version from Github, by'
b'running'
b''
b'::'
b''
b' pip install git+git://github.com/msmexplorer/msmexplorer.git#egg=msmexplorer'
b''
b'Development'
b'-----------'
b''
b'All development happens here, on'
b'`Github <https://github.com/msmexplorer/msmexplorer>`__.'
b''
b"If you're interested in contributing to MSMExplorer, please refer to our"
b'`Contributing <http://msmbuilder.org/msmexplorer/development/contributing.html>`__'
b'guide.'
b''
b'Support'
b'-------'
b''
b'Please'
b'`submit <https://github.com/msmexplorer/msmexplorer/issues/new>`__ any'
b'bugs or questions to the Github issue tracker.'
b''
b'License'
b'-------'
b''
b'Released under a MIT license'
b''
b'Citing'
b'------'
b''
b'.. code:: bibtex'
b''
b' @misc{msmexplorer,'
b" author = {Hern{\\'{a}}ndez, Carlos and"
b' Harrigan, Matthew and'
b' Pande, Vijay},'
b' title = {msmexplorer/msmexplorer: MSMExplorer 0.3},'
b' month = oct,'
b' year = 2016,'
b' doi = {10.5281/zenodo.162942},'
b' url = {https://doi.org/10.5281/zenodo.162942}'
b' }'
b''
b'.. |Build Status| image:: https://travis-ci.org/msmexplorer/msmexplorer.svg?branch=master'
b' :target: https://travis-ci.org/msmexplorer/msmexplorer'
b'.. |Build status| image:: https://ci.appveyor.com/api/projects/status/038hirce0vlx2847?svg=true'
b' :target: https://ci.appveyor.com/project/cxhernandez/msmexplorer'
b'.. |Coverage Status| image:: https://coveralls.io/repos/github/msmexplorer/msmexplorer/badge.svg?branch=master'
b' :target: https://coveralls.io/github/msmexplorer/msmexplorer?branch=master'
b'.. |PyPI version| image:: https://badge.fury.io/py/msmexplorer.svg'
b' :target: http://badge.fury.io/py/msmexplorer'
b'.. |License| image:: https://img.shields.io/badge/license-MIT-red.svg?style=flat'
b' :target: https://opensource.org/licenses/MIT'
b'.. |Documentation| image:: https://img.shields.io/badge/docs-latest-blue.svg?style=flat'
b' :target: http://msmbuilder.org/msmexplorer/'
b'.. |DOI| image:: https://zenodo.org/badge/47228682.svg'
b' :target: https://zenodo.org/badge/latestdoi/47228682'
b''

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

msmexplorer-1.0.0.tar.gz (13.3 kB view hashes)

Uploaded Source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page